The molecular genetics of human hemoglobins

From Water to Land: The Structural Construction and Molecular Switches in Lungs during Metamorphosis of Microhyla fissipes

Simple Summary

The functionalization of lungs is a necessity for most anurans to breathe on land. Previous studies have focused on the morphological and physiological functions of amphibian lungs, while the microstructural changes and molecular mechanisms that underpin the functional maturation of lungs remain under-researched. We used integrated histology and transcriptomics to study the critical cytological and molecular events associated with lung maturation in Microhyla fissipes. The results illuminated the molecular processes and their coordination in lung development, providing an insight into the transition of amphibians from aquatic to terrestrial life stages.

Abstract

Most anurans must undergo metamorphosis to adapt to terrestrial life. This process enhances the air-breathing ability of the lungs to cope with the change in oxygen medium from water to air. Revealing the structural construction and molecular switches of lung organogenesis is essential to understanding the realization of the air-breathing function. In this study, histology and transcriptomics were conducted in combination to explore these issues in Microhyla fissipes’ lungs during metamorphosis. During the pro-metamorphic phase, histological structural improvement of the alveolar wall is accompanied by robust substrate metabolism and protein turnover. The lungs, at the metamorphic climax phase, are characterized by an increased number of cilia in the alveolar epithelial cells and collagenous fibers in the connective tissues, corresponding to the transcriptional upregulation of cilia and extracellular matrix-related genes. Post-metamorphic lungs strengthen their contracting function, as suggested by the thickened muscle layer and the upregulated expression of genes involved in muscle contraction. The blood–gas barrier is fully developed in adult lungs, the transcriptional features of which are tissue growth and regulation of differentiation and immunity. Importantly, significant transcriptional switches of pulmonary surfactant protein and hemoglobin facilitate air breathing. Our results illuminated four key steps of lung development for amphibians to transition from water to land.

Expansion of gene clusters, circular orders, and the shortest Hamiltonian path problem

Clusters of paralogous genes such as the famous HOX cluster of developmental transcription factors tend to evolve by stepwise duplication of its members, often involving unequal crossing over. Gene conversion and possibly other mechanisms of concerted evolution further obfuscate the phylogenetic relationships. As a consequence, it is very difficult or even impossible to disentangle the detailed history of gene duplications in gene clusters. In this contribution we show that the expansion of gene clusters by unequal crossing over as proposed by Walter Gehring leads to distinctive patterns of genetic distances, namely a subclass of circular split systems. Furthermore, when the gene cluster was left undisturbed by genome rearrangements, the shortest Hamiltonian paths with respect to genetic distances coincide with the genomic order. This observation can be used to detect ancient genomic rearrangements of gene clusters and to distinguish gene clusters whose evolution was dominated by unequal crossing over within genes from those that expanded through other mechanisms.

Excitotoxic and Radiation Stress Increase TERT Levels in the Mitochondria and Cytosol of Cerebellar Purkinje Neurons

Telomerase reverse transcriptase (TERT) is the catalytic subunit of telomerase, an enzyme that elongates telomeres at the ends of chromosomes during DNA replication. Recently, it was shown that TERT has additional roles in cell survival, mitochondrial function, DNA repair, and Wnt signaling, all of which are unrelated to telomeres. Here, we demonstrate that TERT is enriched in Purkinje neurons, but not in the granule cells of the adult mouse cerebellum. TERT immunoreactivity in Purkinje neurons is present in the nucleus, mitochondria, and cytoplasm. Furthermore, TERT co-localizes with mitochondrial markers, and immunoblot analysis of protein extracts from isolated mitochondria and synaptosomes confirmed TERT localization in mitochondria. TERT expression in Purkinje neurons increased significantly in response to two stressors: a sub-lethal dose of X-ray radiation and exposure to a high glutamate concentration. While X-ray radiation increased TERT levels in the nucleus, glutamate exposure elevated TERT levels in mitochondria. Our findings suggest that in mature Purkinje neurons, TERT is present both in the nucleus and in mitochondria, where it may participate in adaptive responses of the neurons to excitotoxic and radiation stress.

Calibration of the HemoCue point-of-care analyser for determining haemoglobin concentration in a lizard and a fish

Haemoglobin concentration ([Hb]) is measured for a wide variety of animal studies. The use of point-of-care devices, such as the HemoCue, is becoming increasingly common because of their portability, relative ease of use and low cost. In this study, we aimed to determine whether the [Hb] of blue-tongued skink (Tiliqua nigrolutea) blood can be determined accurately using the HemoCue and whether the HemoCue overestimates the [Hb] of reptile blood in a similar manner to fish blood. Additionally, we aimed to test whether ploidy affected [Hb] determined by the HemoCue using blood from diploid and triploid Atlantic salmon (Salmo salar). The HemoCue Hb 201(+) systematically overestimated [Hb] in both blue-tongued skinks and Atlantic salmon, and there was no difference between calibration equations determined for diploid or triploid salmon. The overestimation was systematic in both species and, as such, [Hb] determined by the HemoCue can be corrected using appropriate calibration equations.

Evolution of hemoglobin and its genes

Insights into the evolution of hemoglobins and their genes are an abundant source of ideas regarding hemoglobin function and regulation of globin gene expression. This article presents the multiple genes and gene families encoding human globins, summarizes major events in the evolution of the hemoglobin gene clusters, and discusses how these studies provide insights into regulation of globin genes. Although the genes in and around the α-like globin gene complex are relatively stable, the β-like globin gene clusters are more dynamic, showing evidence of transposition to a new locus and frequent lineage-specific expansions and deletions. The cis-regulatory modules controlling levels and timing of gene expression are a mix of conserved and lineage-specific DNA, perhaps reflecting evolutionary constraint on core regulatory functions shared broadly in mammals and adaptive fine-tuning in different orders of mammals.

Concise review: production of cultured red blood cells from stem cells

In the Western world, the volunteer-based collection system covers most transfusion needs, but transient shortages regularly develop and blood supplies are vulnerable to potentially major disruptions. The production of cultured red blood cells from stem cells is slowly emerging as a potential alternative. The various cell sources, the niche applications most likely to reach the clinic first, and some of the remaining technical issues are reviewed here.

Novel telomerase-increasing compound in mouse brain delays the onset of amyotrophic lateral sclerosis

Telomerase is expressed in the neonatal brain, in distinct regions of adult brain, and was shown to protect developing neurons from apoptosis. Telomerase reactivation by gene manipulation reverses neurodegeneration in aged telomerase-deficient mice. Hence, we and others hypothesized that increasing telomerase expression by pharmaceutical compounds may protect brain cells from death caused by damaging agents. In this study, we demonstrate for the first time that the novel compound AGS-499 increases telomerase activity and expression in the mouse brain and spinal cord (SC). It exerts neuroprotective effects in NMDA-injected CD-1 mice, delays the onset and progression of the amyotrophic lateral sclerosis (ALS) disease in SOD1 transgenic mice, and, after the onset of ALS, it increases the survival of motor neurons in the SC by 60%. The survival of telomerase-expressing cells (i.e. motor neurons), but not telomerase-deficient cells, exposed to oxidative stress was increased by AGS-499 treatment, suggesting that the AGS-499 effects are telomerase-mediated. Therefore, a controlled and transient increase in telomerase expression and activity in the brain by AGS-499 may exert neuroprotective effects.

Transcriptional regulation of fetal to adult hemoglobin switching: new therapeutic opportunities

In humans, embryonic, fetal, and adult hemoglobins are sequentially expressed in developing erythroblasts during ontogeny. For the past 40 years, this process has been the subject of intensive study because of its value to enlighten the biology of developmental gene regulation and because fetal hemoglobin can significantly ameliorate the clinical manifestations of both sickle cell disease and β-thalassemia. Understanding the normal process of loss of fetal globin expression and activation of adult globin expression could potentially lead to new therapeutic approaches for these hemoglobin disorders. Herein, we briefly review the history of the study of hemoglobin switching and then focus on recent discoveries in the field that now make new therapeutic approaches seem feasible in the future. Erythroid-specific knockdown of fetal gene repressors or enforced expression of fetal gene activators may provide clinically applicable approaches for genetic treatment of hemoglobin disorders that would benefit from increased fetal hemoglobin levels.

Mir-144 selectively regulates embryonic alpha-hemoglobin synthesis during primitive erythropoiesis

Precise transcriptional control of developmental stage-specific expression and switching of alpha- and beta-globin genes is significantly important to understand the general principles controlling gene expression and the pathogenesis of thalassemia. Although transcription factors regulating beta-globin genes have been identified, little is known about the microRNAs and trans-acting mechanism controlling alpha-globin genes transcription. Here, we show that an erythroid lineage-specific microRNA gene, miR-144, expressed at specific developmental stages during zebrafish embryogenesis, negatively regulates the embryonic alpha-globin, but not embryonic beta-globin, gene expression, through physiologically targeting klfd, an erythroid-specific Krüppel-like transcription factor. Klfd selectively binds to the CACCC boxes in the promoters of both alpha-globin and miR-144 genes to activate their transcriptions, thus forming a negative feedback circuitry to fine-tune the expression of embryonic alpha-globin gene. The selective effect of the miR-144-Klfd pathway on globin gene regulation may thereby constitute a novel therapeutic target for improving the clinical outcome of patients with thalassemia.

OmpA is an adhesion factor of Aeromonas veronii, an optimistic pathogen that habituates in carp intestinal tract

AIMS

In the present study, we focused on one of the Aeromonas veronii isolates that exhibited marked adhesion onto carp intestine and studied its membrane-associated proteins for their possible involvement in mucosal adhesion.

METHODS AND RESULTS

We isolated a strain of Aer. veronii (CWP11) that exhibited a high degree of temperature-dependent adhesion activity onto carp intestinal tract and studied its adhesion factor. A proteomic analysis of the membrane-associated fraction showed the presence of multiple proteins that were specifically expressed in CWP11 cells cultured at 25 degrees C. Of these, a 30 kDa protein was identified to be OmpA by a mass fingerprint analysis. Cloning and nucleotide sequencing of the ompA region of CWP11 revealed the presence of two tandem ompA homologues (ompAI-ompAII). Escherichia coli that expressed either OmpAI or OmpAII exhibited marked adhesion onto carp intestinal surface. Disruption of ompAI by a homologous recombination technique resulted in marked reduction of the adhesion activity in CWP11.

CONCLUSION

The OmpA homologue plays an important role in the adhesion of the Aer. veronii strain onto the surface of intestinal tract.

SIGNIFICANCE AND IMPACT OF THE STUDY

We successfully identified an OmpA homologue to be an adhesion factor of Aer. veronii, an optimistic pathogen that habituates in carp intestinal tract.

Organisation of the Hb 1 genes of the Antarctic skate Bathyraja eatonii: new insights into the evolution of globin genes

An extensive investigation of the organisation of globin genes has greatly contributed to the understanding of universal mechanisms of gene evolution and expression. Cartilaginous fish are the first organisms that have evolved the tetrameric form of hemoglobin (Hb). So far, there has been absolute lack of data about globin genes in chondrichthyans. Bathyraja is the dominant rajid south of 60 degrees S. In the framework of the investigations on globin genes of Antarctic red-blooded and Hb-less fish we obtained the cloning of the alpha- and beta-globin cDNAs of the main Hb (Hb 1) of the skate Bathyraja eatonii. Then, a genomic fragment of 6.2 kb was isolated where the Hb 1 alpha and beta genes are linked in a tail-to-head (3' to 5') orientation. The beta-globin gene promoter region and the chromosomal organisation of the Hb 1 genes of B. eatonii have been compared to their homologues in other vertebrates. The finding of a tail-to-head linkage of the Hb 1 alpha- and beta-globin genes in B. eatonii is the first characterisation of the organisation of globin genes in chondrichthyes; such finding offers a novel contribution to the understanding of the evolution of this class of genes. Moreover, the characterisation of chondrichthyan genes is very important for gaining insight into the ancestral state of vertebrate genomes.

Mapping of alpha- and beta-globin genes on Antarctic fish chromosomes by fluorescence in-situ hybridization

The pathways and mechanisms of genomic change that have led to the peculiar haemoglobinless phenotype of the white-blooded Antarctic icefishes (16 species in the family Channichthyidae) constitute an important model for understanding the rapid diversification of the Antarctic notothenioid fish flock. To provide complementary structural information on genomic change at globin-gene loci in Antarctic fish species, cytogenetic studies and in-situ chromosomal mapping have been undertaken. Using a DNA probe containing one alpha- and one beta-globin gene from the embryonic/juvenile globin gene cluster of the red-blooded species Notothenia coriiceps, we mapped the cluster on the chromosomes of Antarctic teleosts by fluorescence in-situ hybridization. As anticipated on the basis of its molecular organization, the cluster was located on a single chromosome pair in all of the red-blooded fish species probed (N. coriiceps, N. angustata, Trematomus hansoni, T. pennellii). In contrast, the alpha/beta-globin probe did not recognize complementary sequences on the chromosomes of the white-blooded species Chionodraco hamatus and Channichthys rhinoceratus. These results represent the first example of chromosomal mapping of embryonic/juvenile globin genes in teleostean fishes. Beyond its relevance to the evolutionary history of Antarctic notothenioids, this work contributes to our understanding of the evolution of the chromosomal loci of globin genes in fishes and other vertebrates.

Characterization of embryonic globin genes of the zebrafish

Hemoglobin switching is a complex process by which distinct globin chains are produced during stages of development. In an effort to characterize the process of hemoglobin switching in the zebrafish model system, we have isolated and characterized several embryonic globin genes. The embryonic and adult globin genes are found in clusters in a head-to-head configuration. One cluster of embryonic and adult genes is localized to linkage group 3, whereas another embryonic cluster is localized on linkage group 12. Several embryonic globin genes demonstrate an erythroid-specific pattern of expression early during embryogenesis and later are downregulated as definitive hematopoiesis occurs. We utilized electrospray mass spectroscopy to correlate globin genes and protein expression in developing embryonic red cells. The mutation, zinfandel, has a hypochromic microcytic anemia as an embryo, but later recovers in adulthood. The zinfandel gene maps to linkage group 3 near the major globin gene locus, strongly suggesting that zinfandel represents an embryonic globin defect. Our studies are the first to systematically evaluate the embryonic globins in the zebrafish and will ultimately be useful in evaluating zebrafish mutants with defects in hemoglobin production and switching.

A retroviral repetitive element confers tissue-specificity to the human alcohol dehydrogenase 1C (ADH1C) gene

The human ADH1A, ADH1B, and ADH1C genes encode alcohol dehydrogenases (ADHs) that metabolize ethanol. They evolved by recent tandem duplications and have similar proximal cis-acting elements, but differ in tissue-specificity. We hypothesized that distal cis-acting elements confer tissue-specificity. In this article, we identify multiple cis-acting elements in the ADH1C upstream region. Negative elements in the fragments from bp -1,078 to -622 and from bp -3,957 to -2,651 decreased transcription activity to 41 and 14%, respectively. A tissue-specific regulatory element in the region between bp -1,503 and -1,053 stimulated transcription sixfold in H4IIE-C3 hepatoma cells but reduced transcription to 23% in HeLa cells. This regulatory element was mapped to a repetitive sequence that is similar to the U3 repeat within the long terminal repeat of human endogenous retrovirus ERV9. The 30-fold difference in expression between two cell lines demonstrates that this upstream U3 element, which inserted after the duplications that created the three class I ADH genes, plays an important role in regulating tissue-specificity of ADH1C. The ubiquitous Nuclear factor-Y (NF-Y) and an H4IIE-C3/liver-specific factor bound to the subrepeat sequence. This result suggested that tissue specificity might result from combinatorial regulation by these two transcription factors.

Regulation of the mammalian alcohol dehydrogenase genes

This review focuses on the regulation of the mammalian medium-chain alcohol dehydrogenase (ADH) genes. This family of genes encodes enzymes involved in the reversible oxidation of alcohols to aldehydes. Interest in these enzymes is increased because of their role in the metabolism of beverage alcohol as well as retinol, and their influence on the risk for alcoholism. There are six known classes ADH genes that evolved from a common ancestor. ADH genes differ in their patterns of expression: most are expressed in overlapping tissue-specific patterns, but class III ADH genes are expressed ubiquitously. All have proximal promoters with multiple cis-acting elements. These elements, and the transcription factors that can interact with them, are being defined. Subtle differences in sequence can affect affinity for these factors, and thereby influence the expression of the genes. This provides an interesting system in which to examine the evolution of tissue specificity. Among transcription factors that are important in multiple members of this gene family are the C/EBPs, Sp1,USF, and AP1, HNF-1, CTF/NF-1, glucocorticoid, and retinoic acid receptors, and several as-yet unidentified negative elements, are important in at least one of the genes. There is evidence that cis-acting elements located far from the proximal promoter are necessary for proper expression. Three of the genes have upstream AUGs in the 5' nontranslated regions of their mRNA, unusual for mammalian genes. The upstream AUGs have been shown to significantly affect expression of the human ADH5 gene.

Heterogeneity and differential expression under hypoxia of two-domain hemoglobin chains in the water flea, Daphnia magna

Hemoglobin (Hb) purified from the water flea, Daphnia magna, reared under hypoxia was analyzed by two-dimensional gel electrophoresis. The Hb was shown to be composed of six major subunit chain species (designated as DHbA to DHbF). The NH2-terminal amino acid sequences of DHbA, DHbB, DHbC, and DHbF are different from one another, indicating that at least four Hb genes are present in D. magna. The NH2-terminal amino acid sequences of DHbD and DHbE are the same as those of DHbA and DHbB, respectively. The six Hb chains were also found in the animal reared under normoxia in small amounts and with altered composition; the extent of decrease under normoxia was higher in the amounts of DHbC, DHbD, and DHbF than those of others. These results indicate that the Hb genes are differentially regulated by the ambient oxygen concentration. Four Hb genes constituting a cluster in the order, dhb4, dhb3, dhb1, and dhb2, were found on the chromosome of D. magna. The complete nucleotide sequences of the dhb1, dhb2, and dhb3 genes and their cDNAs showed that the genes have a seven-exon, six-intron structure. The structure consists of an intron separating an exon encoding a secretory signal sequence, two large repeated regions of a three-exon, two-intron structure that encode each a domain containing a heme-binding site, and an intron bridging the two repeated regions. The deduced amino acid sequences of the gene products showed higher than 79% identity to one another and showed unique features conserved in D. magna Hb chains. The analysis also suggested that DHbB (or DHbE), DHbF, and DHbC are encoded by the dhb1, dhb2, and dhb3 genes, respectively.

Pathological consequences of sequence duplications in the human genome

As large-scale sequencing accumulates momentum, an increasing number of instances are being revealed in which genes or other relatively rare sequences are duplicated, either in tandem or at nearby locations. Such duplications are a source of considerable polymorphism in populations, and also increase the evolutionary possibilities for the coregulation of juxtaposed sequences. As a further consequence, they promote inversions and deletions that are responsible for significant inherited pathology. Here we review known examples of genomic duplications present on the human X chromosome and autosomes.

MARs mission update

Genes are organized as chromatin domains and positioned in the nucleus through regions of nuclear matrix association, termed MARs. Although well-studied, the mechanisms regulating expression of the beta-globin locus remain an enigma. Here, we show that certain MAR sequences of the beta-globin locus are conserved and reiterated throughout the genome in association with other genes of the hematopoietic lineage. Further, the density of the MARs within the beta-globin locus and the sharing of these sequences by the various members of this gene cluster suggest that they may provide critical gene regulatory components.

Head-to-head linkage of carp alpha- and beta-globin genes

The alpha- and beta-globin gene variants are believed to have diverged from a single ancestral globin gene, and the divergence was primed by the duplication of the ancestral globin gene. To understand the process of gene duplication, we investigated the alpha- and beta-globin gene arrangement of a bony fish (carp). From a Southern analysis of seven previously prepared lambda phage clones (lambdaCG1-7) using radio-labelled alpha- or beta-globin gene probes, it was found that the clones included both the alpha- and beta-globin genes, and that they were located within a distance of 1 kb. Additionally, the linkage of two alpha-globin genes and two beta-globin genes in the clone lambdaCG1, 5 and 7 (e.g., alpha-beta-alpha-beta in lambdaCG5) revealed an arrangement that is different from the arrangement in higher vertebrates in which the alpha-globin and beta-globin genes generally occur at different loci. The distances between the detached alpha- to beta-globin genes were approximately 5 to 10 kb. DNA sequencing of the adjacently linked alpha- and beta-globin genes in lambdaCG3 showed that they were arranged in a head-to-head orientation. PCR amplification using primers for the internal region between the carp alpha- and beta-globin genes gave approximately 0.9-kb products from each of the clones lambdaCG1, 3, 4, 5, 6, and 7, and from the chromosomal DNA of German mirror carp, Saku carp, Suwa carp, and Yamato carp. This demonstrates the alternative arrangement of carp alpha- and beta-genes in the globin gene locus (i.e., 3'alpha5'-5'beta3'-3'alpha5'-5'beta3' in lambdaCG5), and the widespread distribution of head-to-head-linked alpha- and beta-globin genes in carp. Based on the above results, we hypothesize that the duplication of the ancestral globin gene (prior to the divergence of the a and beta forms) occurred in a head-to-head direction.

Homologous recombination of a flanking repeat gene cluster is a mechanism for a common contiguous gene deletion syndrome

Smith-Magenis syndrome (SMS), caused by del(17)p11.2, represents one of the most frequently observed human microdeletion syndromes. We have identified three copies of a low-copy-number repeat (SMS-REPs) located within and flanking the SMS common deletion region and show that SMS-REP represents a repeated gene cluster. We have isolated a corresponding cDNA clone that identifies a novel junction fragment from 29 unrelated SMS patients and a different-sized junction fragment from a patient with dup(17)p11.2. Our results suggest that homologous recombination of a flanking repeat gene cluster is a mechanism for this common microdeletion syndrome.

Repair pattern in the beta-globin gene cluster of human fibroblasts after ultraviolet irradiation

We have developed a novel technique to determine repair of structurally different DNA lesions. It was used to address the question of whether DNA repair in the absence of transcription occurs in a uniformly random manner or with preferences for certain regions. Human fibroblasts were exposed to ultraviolet light (3-10 J/m2) and treated with 7.5 mM hydroxyurea to inhibit replicative DNA synthesis. During the first hours after irradiation cells were treated with 5-bromodeoxyuridine to label the regions undergoing repair, with the presumption that the regions that have been more efficiently repaired would incorporate more of the nucleoside. A 155-kb DNA sequence containing the entire human beta-globin domain was reconstructed using sequences deposited in the EMBL gene bank. Twelve uniformly long single-copy RNA probes spanning the beta-globin cluster were synthesised in vitro and immobilized on microtiter plates. They were hybridized with DNA from the irradiated cells. The amount of 5-bromodeoxyuridine, incorporated as a result of repair in the DNA fractions hybridized to the different RNA probes, was determined immunochemically using antibody to this nucleoside. By this technique we registered increased repair efficiency in the zone of the permanent scaffold attachment region at the 5'-end of the beta-globin domain during the first hours after ultraviolet irradiation. This result was confirmed and by the more conventional T4 endonuclease V technique detecting the removal of cyclobutane pyrimidine dimers.

Organization and expression of canine olfactory receptor genes

Four members of the canine olfactory receptor gene family were characterized. The predicted proteins shared 40-64% identity with previously identified olfactory receptors. The four subfamilies identified in Southern hybridization experiments had as few as 2 and as many as 20 members. All four genes were expressed exclusively in olfactory epithelium. Expression of multiple members of the larger subfamilies was detected, suggesting that most if not all of the cross-hybridizing bands in genomic Southern blots represented actively transcribed olfactory receptor genes. Analysis of large DNA fragments using Southern blots of pulsed-field gels indicated that subfamily members were clustered together, and that two of the subfamilies were closely linked in the dog genome. Analysis of the four olfactory receptor gene subfamilies in 26 breeds of dog provided evidence that the number of genes per subfamily was stable in spite of differential selection on the basis of olfactory acuity in scent hounds, sight hounds, and toy breeds.

A physical map of the Q region of B1O.P

The murine class I MHC Q region is part of a large complex multigene family whose members have various peptide binding functions. The structure of the Q region is complex, varying extensively in the b, d, k, and q haplotypes so far examined. To better understand the structural heterogeneity, we examined the Q region of B 10.P, a strain whose immunological characteristics are distinct from other haplotypes. A total of 89 cosmids were isolated from genomic DNA. The B 10.P Q region was found to contain seven genes in a 190-kb cluster linked to DP and two additional Q genes in a separate 55-kb cluster. The gene arrangement in this haplotype was unique and did not correspond to any other haplotype; this underscores the complexity of chromosomal structure in this region. In addition to the Q region clusters, Tla region was tentatively aligned in five clusters spanning approximately 300 kb. One 37-kb M region cosmid was also identified.

Molecular evolution of duplicate copies of genes encoding cytosolic glutamine synthetase in Pisum sativum

Here, we describe two nearly identical expressed genes for cytosolic glutamine synthetase (GS3A and GS3B) in Pisum sativum L. RFLP mapping data indicates that the GS3A and GS3B genes are separate loci located on different chromosomes. DNA sequencing of the GS3A and GS3B genes revealed that the coding regions are 99% identical with only simple nucleotide substitutions resulting in three amino acid differences. Surprisingly, the non-coding regions (5' non-coding leader, the 11 introns, and 3' non-coding tail) all showed a high degree of identity (96%). In these non-coding regions, 25% of the observed differences between the GS3A and GS3B genes were deletions or duplications. The single difference in the 3' non-coding regions of the GS3A and GS3B genes was a 25 bp duplication of an AU-rich element in the GS3B gene. As the GS3B mRNA accumulates to lower levels than the GS3A gene, we tested whether this sequence which resembles an mRNA instability determinant functioned as such in the context of the GS mRNA. Using the GS3B 3' tail as part of a chimeric gene in transgenic plants, we showed that this AU-rich sequence has little effect on transgene mRNA levels. To determine whether the GS3A/GS3B genes represent a recent duplication, we examined GS3-like genes in genomic DNA of ancient relatives of P. sativum. We observed that several members of the Viceae each contain two genomic DNA fragments homologous to the GS3B gene, suggesting that this is an ancient duplication event. Gene conversion has been invoked as a possible mechanism for maintaining the high level of nucleotide similarity found between GS3A and GS3B genes. Possible evolutionary reasons for the maintenance of these 'twin' GS genes in pea, and the general duplication of genes for cytosolic GS in all plant species are discussed.

Genetic determinants of human hypertension

Hypertension is a common trait of multifactorial determination imparting an increased risk of myocardial infarction, stroke, and end-stage renal disease. The primary determinants of hypertension, as well as the factors which determine specific morbid sequelae, remain unknown in the vast majority of subjects. Knowledge that a large fraction of the interindividual variation in this trait is genetically determined motivates the application of genetic approaches to the identification of these primary determinants. Success in this effort will afford insights into pathophysiology, permit preclinical identification of subjects with specific inherited susceptibility, and provide opportunities to tailor therapy to specific underlying abnormalities. To date, mutations in three genes have been implicated in the pathogenesis of human hypertension: mutations resulting in ectopic expression of aldosterone synthase enzymatic activity cause a mendelian form of hypertension known as glucocorticoid-remediable aldosteronism; mutations in the beta subunit of the amiloride-sensitive epithelial sodium channel cause constitutive activation of this channel and the mendelian form of hypertension known as Liddle syndrome; finally, common variants at the angiotensinogen locus have been implicated in the pathogenesis of essential hypertension in Caucasian subjects, although the nature of the functional variants and their mechanism of action remain uncertain. These early findings demonstrate the feasibility and utility of the application of genetic analysis to dissection of this trait.

Hypertension caused by a truncated epithelial sodium channel gamma subunit: genetic heterogeneity of Liddle syndrome

Sensitivity of blood pressure to dietary salt is a common feature in subjects with hypertension. These features are exemplified by the mendelian disorder, Liddle's syndrome, previously shown to arise from constitutive activation of the renal epithelial sodium channel due to mutation in the beta subunit of this channel. We now demonstrate that this disease can also result from a mutation truncating the carboxy terminus of the gamma subunit of this channel; this truncated subunit also activates channel activity. These findings demonstrate genetic heterogeneity of Liddle's syndrome, indicate independent roles of beta and gamma subunits in the negative regulation of channel activity, and identify a new gene in which mutation causes a salt-sensitive form of human hypertension.

Amplification of the murine mdr2 gene and a reconsideration of the structure of the murine mdr gene locus

A common feature of cells selected in vitro for the multidrug resistance (MDR) phenotype is the amplification and concomitant overexpression of the mdr genes. In murine macrophage-like J774.2-derived MDR cell lines, there is a good correlation between levels of amplification and expression for the mdr1b gene, but not for the other two gene family members, mdr1a and mdr2. To understand this phenomenon better, a study of the amplification and expression of the mdr2 gene was undertaken. Southern blotting of genomic DNAs from a series of six MDR cell lines revealed that five of these lines had 5'-end amplification of mdr2, whereas only three contained 3'-end amplification. The analysis also suggested the involvement of a recombination hot-spot in this phenomenon. Despite the observation that the ratio between the number of copies of the 5' and 3' ends of the gene differs among cell lines, the ratio of 5' to 3' end transcription of mdr2 was approximately 1 in all cell lines. An analysis of promoter methylation in MDR cell lines demonstrated that this mechanism may play a role in regulating the transcription of mdr2, but not of mdr1b. Long-range mapping of the mdr locus in parental and amplified cell lines suggested that the three mdr genes are oriented in the same direction, and also revealed the presence of a number of rearrangement events. Models for the murine mdr gene locus in wild-type cells and in a cell line containing a rearrangement are presented.

Collagen IV alpha 3, alpha 4, and alpha 5 chains in rodent basal laminae: sequence, distribution, association with laminins, and developmental switches

Collagen IV is a major component of vertebrate basal laminae (BLs). Studies in humans have revealed a family of genes encoding alpha 1-alpha 6 collagen IV chains and implicated alpha 3-alpha 6 in disease processes (Goodpasture and Alport syndromes and diffuse leiomyomatosis). To extend studies of these components to an experimentally accessible animal, we cloned cDNAs encoding partial collagen alpha 3, alpha 4, and alpha 5(IV) chains from the mouse. Ribonuclease protection assays showed that all three genes were expressed at highest levels in kidney and lung; alpha 5(IV) was also expressed at high levels in heart. We then made antibodies specific for each collagen IV chain. Immunohistochemical studies of several tissues revealed many combinations of collagen IV chains; however, alpha 3 and alpha 4 (IV) were always coexpressed, and only appeared in BLs that were alpha 5(IV) positive. The alpha 3-alpha 5(IV) chains were frequently but not exclusively associated with the S (beta 2) chain of laminin, as were the alpha 1, 2 (IV) collagen chains with laminin B1 (beta 1). An analysis of developing rat kidney BLs showed that newly formed (S-shaped) nephrons harbored collagen alpha 1 and alpha 2(IV) and laminin B1; maturing (capillary loop stage) BLs contained collagen alpha 1-alpha 5(IV) and laminin B1 and S-laminin; and mature glomerular BLs contained mainly collagen alpha 3-alpha 5(IV) and S-laminin. Thus, collagen alpha 1 and alpha 2(IV) and laminin B1 appear to be fetal components of the glomerular BL, and there is a developmental switch to collagen alpha 3-alpha 5(IV) and S-laminin expression.

The evolution and recognition of protein sequence repeats

Many proteins sequences contain motifs which display similarity. The similarities between the repeats are a result of gene duplication and/or gene fusion. The evolutionary role of repeats within protein sequences is considered and some repeat examples are given ranging from tandem repeats to multiple types of repeats which are sequentially interspersed. Existing computer methods to delineate repeats in individual protein sequences are discussed and a novel sensitive repeat recognition method is introduced.

Characterization of a hair (wool) keratin intermediate filament gene domain

In epithelial differentiation keratin intermediate filament genes are expressed in multifarious tissue-specific and stage-specific patterns. Pairs of type I and type II intermediate filament genes, belonging to multigene families, are coordinately regulated, and 4-5 genes of each type are expressed in the hair follicle. Accumulating chromosomal mapping data points to a major locus for each intermediate filament multigene family on separate chromosomes. In this report we describe the isolation of a sheep hair keratin cosmid by chromosome walking that overlaps two previously described cosmids and establishes a continuous 100-kb segment of cloned DNA containing three hair and three hair-like type II intermediate filament keratin genes. A new hair keratin type II intermediate filament gene, KRT2.11, is located in the middle of the cluster, and partial sequence data reveal a striking conservation of its predicted N-terminal region with other sheep hair keratin type II intermediate filament proteins. Expression analyses demonstrate the presence of a 2.4-kb KRT2.11 transcript in wool follicle RNA and show that expression occurs in the follicle cortical keratinocytes above the dermal papilla. The three hair genes are clustered within about 40 kb and flanked by hair-like genes that are not expressed in the hair follicle, thereby demarcating a hair keratin gene domain.

Tissue- and stratum-specific expression of the human involucrin promoter in transgenic mice

Involucrin is a marker of keratinocyte terminal differentiation and is expressed only in the suprabasal layers of stratified squamous epithelium. In a previous study with various cell types in culture, we noted that expression of the putative human involucrin promoter was keratinocyte specific. To determine if this promoter is sufficient to direct expression to the suprabasal cells of stratified squamous epithelia in vivo, we have now generated transgenic mouse lines harboring the involucrin promoter sequences linked to a beta-galactosidase reporter gene. In the resulting lines, beta-galactosidase was expressed in the suprabasal compartment of stratified squamous epithelia and in hair follicles in a tissue-specific manner. In the palate, distinct vertical stacks of beta-galactosidase-expressing cells were present, suggesting movement of clonally derived cells through the epithelium. The involucrin gene has a single intron upstream of the translational start site, and removal of this intron did not affect tissue- or stratum-specific expression. These results show that the 3.7-kb involucrin upstream sequences contain all the information necessary for a high level of tissue- and stratum-specific expression.

Transcriptional characterization of an alpha-zein gene cluster in maize

A cluster of five alpha-zein subfamily 4 (alpha-zein SF4) genes are present in a 56 kb region of the maize W22 genome. Two types of alpha-zein SF4 genes are in the cluster. One of the genes, termed a type 1 (T1) alpha-zein SF4 gene, contains no early in-frame stop codons. Four of the genes, termed type 2 (T2) alpha-zein SF4 genes, contain one or two early in-frame stop codons. The base sequence of the T1 alpha-zein SF4 gene is similar (> 90%) to the sequences of any of the four T2 alpha-zein SF4 genes. However, their sequences differ markedly at distances greater than -875 bp upstream from the translation initiation codon of the alpha-zein coding region. This region of dissimilarity is well inside the functional 5'-flanking region for the genes since a 1.8 kb transcript is initiated in this region and the sequences of the T2 alpha-zein SF4 genes are similar in this region. Two sizes of mRNA transcripts, 1.8 kb and 0.9 kb, were detected in a gene specific manner for 4 of the 5 genes in this alpha-zein SF4 gene cluster. One of the T2 alpha-zein SF4 genes had only the 0.9 kb transcript. The RNA level for the 0.9 kb transcript of the T1 alpha-zein SF4 gene was 5- to 10-fold higher than the transcript levels of any of the T2 alpha-zein SF4 genes. In each case, the amount of the 0.9 kb transcript detected was at least 5-fold higher than the amount of the 1.8 kb transcript. A cDNA clone with a sequence identical to a T2 alpha-zein SF4 gene was isolated, providing the first direct evidence for the transcription of T2 alpha-zein genes containing early in-frame stop codon(s) in maize endosperm.

CACC box and enhancer response of the human embryonic epsilon globin promoter

The functional interaction between the human epsilon globin promoter and an erythroid-specific transcription enhancer, 5' HS-2, has been analyzed by transient expression assay. While stepwise deletion of DNA sequences between -852 and -122 had only small effects, removal of the CACC box at position -111 greatly decreased epsilon-globin promoter activity, as well as its response to the enhancer function of 5' HS-2 in erythroid cells. Our data demonstrated that the three ubiquitous promoter elements, the CACC, CCAAT, and TATA boxes, of the epsilon-globin-encoding gene together form a minimal promoter that would interact efficiently with 5' HS-2, and that at least the CACC box is an essential functional component of this enhancer-promoter interaction.

Organization of non-vertebrate globin genes

The organization of non-vertebrate globin genes exhibits substantially more variability than the three-exon, two-intron structure of the vertebrate globin genes. (1) The structures of genes of the single-domain globin chains of the annelid Lumbricus and the mollusc Anadara, and the globin gene coding for the two-domain chains of the clam Barbatia, are similar to the vertebrate plan. (2) Genes for single-domain chains exist in bacteria and protozoa. Although the globin gene is highly expressed in the bacterium Vitreoscilla, the putative globin gene hmp in E. coli, which codes for a chimeric protein whose N-terminal moiety of 139 residues contains 67 residues identical to the Vitreoscilla globin, may be either unexpressed or expressed at very low levels, despite the presence of normal regulatory sequences. The DNA sequence of the globin gene of the protozoan Paramecium, determined recently by Yamauchi and collaborators, appears to consist of two exons separated by a short intron. (3) Among the lower eukaryotes, the yeasts Saccharomyces and Candida have chimeric proteins consisting of N-terminal globin and C-terminal flavoprotein moieties of about the same size. The structure of the gene for the chimeric protein of Saccharomyces exhibits no introns. According to Riggs, the presence of chimeric proteins in E. coli and other prokaryotes, such as Alcaligenes and Rhizobium, as well as in yeasts, suggests a previously unrecognized evolutionary pathway for hemoglobin, namely that of a multipurpose heme-binding domain attached to a variety of unrelated proteins with diverse functions. (4) The published globin gene sequences of the insect larva Chironomus have an intron-less structure and are present as clusters of multiple copies; the expression of the globin genes is tissue and developmental stage-specific. Furthermore, the expression of many of these genes has not yet been demonstrated despite the presence of apparently normal regulatory sequences in the two flanking regions. Unexpectedly, Bergtrom and collaborators have recently shown that at least three Ctt globin II beta genes contain putative introns. (5) Pohajdak and collaborators have found a seven-exon and six-intron structure for the globin gene of the nematode Pseudoterranova which codes for a two-domain globin chain. Although the second and fourth introns of the N-terminal domain correspond to the two introns found in vertebrate globin genes, the position of the third intron is close to that of the central intron in plant hemoglobins.(ABSTRACT TRUNCATED AT 400 WORDS)

Genomic organization of an alpha-zein gene cluster in maize

The genes encoding the alpha-zein proteins of maize constitute a large multigene family of some 75 genes. This multigene family can be divided into four subfamilies based on the nucleotide sequences of their genes and the deduced amino acid sequences of their proteins. We describe for the first time evidence of a clustering of five alpha-zein subfamily 4 (SF4) genes that are members of one of the major alpha-zein subfamilies in a 56 kb region of the genome of the maize inbred line W22. None of the other three known alpha-zein gene subfamilies (SF1, SF2, or SF3) are present in this cluster. The genomic region was reconstructed using restriction endonuclease maps to identify and align three overlapping cosmid clones isolated from a genomic library. The alpha-zein genes are not evenly spaced; the minimum distance between genes is 3.5 kb; the maximum is 13 kb. All the alpha-zein genes in the cluster have the same transcriptional orientation. The location and sequences of some of the repetitive DNA elements in this gene cluster were determined. We estimate that there are a minimum of eight repetitive DNA elements in this region. The sequences of the repetitive elements (not functionally defined) are located between or among the alpha-zein genes. The regions containing two of these repetitive elements (Rep1 and Rep4) have been sequenced; they are about 15 kb apart in the genome. These repetitive elements have similar sequences for about 300 bp out of the 400 bp compared. The regions of sequence similarity, however, are in reverse orientation to one another.(ABSTRACT TRUNCATED AT 250 WORDS)

Origin of a "bridge" intron in the gene for a two-domain globin

Red cells of the clam Barbatia reeveana express two hemoglobins, one composed of 16- to 17-kDa chains and the other of 35-kDa chains. The nucleotide sequence of the cDNA encoding the 35-kDa chain shows that the polypeptide has two very similar heme-binding domains, which are joined without use of an additional bridging sequence. Two novel introns occur in the gene for the two-domain globin: one, the "precoding" intron, is located two bases 5' from the start codon, and the other, a "bridge" intron, separates the DNA sequences encoding the two domains. Close correspondence exists between the 3' end of the precoding intron and the 3' end of the bridge intron and between parts of the 3' noncoding region of the cDNA for the two-domain globin and the 5' end of the bridge intron. These observations indicate that the bridge intron arose by unequal crossing-over between two identical or very similar genes for a single-domain globin. This conclusion, together with the proposal that exons were initially independent "minigenes" [Gilbert, W. (1987) Cold Spring Harbor Symp. Quant. Biol. 52, 901-905], suggests that many introns may have evolved from the 5' noncoding region of one gene and/or the 3' noncoding region of a second gene. This hypothesis implies that splice junctions would be associated with the original NH2 and COOH termini of proteins and provides an explanation for the observation that splice junctions usually map to protein surfaces. They do so because most NH2- and COOH-terminal residues are usually located on or near the surfaces of proteins.

The exon-intron organization of the human erythrocyte alpha-spectrin gene

The human erythrocyte alpha-spectrin gene which spans 80 kbp has been cloned from human genomic DNA as overlapping lambda recombinants. The exon-intron junctions were identified and the exons mapped. The gene is encoded by 52 exons whose sizes range from 684 bp to the smallest of 18 bp. The donor and acceptor splice site sequences match the splice site consensus sequences, with the exception of one splice site where a donor sequence begins with -GC. The size and location of exons do not correlate with the 106-amino-acid repeat, except in three locations where the surrounding codons are conserved as well. The lack of correspondence between exons and 106-amino-acid repeat is interpreted to reflect the appearance of a spectrin-like gene from a minigene early in the evolution of eukaryotes. Since current evidence indicates that introns were present in genes before the divergence of prokaryotes and eukaryotes, it is possible that the original distribution of introns within the minigene has been lost by the random deletion of introns from the spectrin gene.

Electrophoretic karyotype and linkage groups of the amoeboflagellate Naegleria gruberi

We have constructed a molecular karyotype for two strains of Naegleria gruberi using pulsed field gel electrophoresis. Each strain has about 23 chromosomes, considerably more than any previous estimate. These chromosomes range in size from 400 kilobasepairs to over 2,000 kilobasepairs. In Naegleria, construction of the DNA karyotype depends on assessment of the anomalous electrophoretic mobility of the circular ribosomal RNA genes. We have determined the chromosomal locations of an identified unique gene (flagellar calmodulin) and four identified multigene families (alpha- and beta-tubulin, actin, ubiquitin), as well as three differentially expressed genes of unknown functions. The ca. 12 actin genes are dispersed over at least seven chromosomes, whereas the majority of the more than eight alpha-tubulin genes are confined to a single chromosome. The ubiquitin genes are found on five chromosomes in one strain and seven in the other and the beta-tubulin genes are on three or four. Our observations provide a foundation for molecular genetic studies in this organism.

Analysis of possible repressor elements in the 5'-flanking region of the human beta-globin gene

Human beta-globin gene expression is confined predominantly to the adult with little or no expression of this gene occurring during embryonic or fetal life. The lack of expression of this gene in embryonic and fetal erythroid tissue could be due to the absence of required positive regulatory factors in these cells or the presence of negative regulatory factors which prevent expression of the adult globin gene. To test the repressor model, we have used a gel electrophoretic mobility shift assay to identify regions in the human beta-globin gene which bind proteins found in K562 cells, a cell line that expresses embryonic and fetal globins but not adult beta-globin. DNA fragments comprising the entire human beta-globin gene were assayed using nuclear proteins from K562 cells, and four regions were found that bind proteins. These are located within the 5'-flanking region, within the first and second introns, and at the 3'-flanking region of the gene. Previous studies have suggested the presence of potential repressor sites 5' of exon 2. For this reason, we examined whether the lack of the binding regions in the 5'-flanking sequence allow expression of the human beta-globin gene in transgenic mice during embryonic life. beta-globin gene expression was confined to adult life, indicating that if a transcriptional repressor is responsible for inactivating this gene in embryonic tissue, it is not regulated solely by sequences upstream from -122 bp in the 5'-flanking region of the human beta-globin gene.

The nucleoskeleton and the topology of transcription

Transcription is conventionally believed to occur by passage of a mobile polymerase along a fixed template. Evidence for this model is derived almost entirely from material prepared using hypotonic salt concentrations. Studies on subnuclear structures isolated using hypertonic conditions, and more recently using conditions closer to the physiological, suggest an alternative. Transcription occurs as the template moves past a polymerase attached to a nucleoskeleton; this skeleton is the active site of transcription. Evidence for the two models is summarised. Much of it is consistent with the polymerase being attached and not freely diffusible. Some consequences of such a model are discussed.

High-level, erythroid-specific expression of the human alpha-globin gene in transgenic mice and the production of human hemoglobin in murine erythrocytes

Using the dominant control region (DCR) sequences that flank the beta-globin gene locus, we have been able to achieve high-level expression of the human alpha-globin gene in transgenic mice. Expression in fetal liver and blood is copy number dependent and at levels comparable to that of the endogenous mouse alpha-globin genes. Transgenic fetuses with high-copy numbers of the transgene suffer severe anemia and die before birth. Using a construct with both the human alpha- and beta-globin genes and the beta-globin DCR, live mice with low-copy numbers were obtained. Both human globin genes are expressed at high levels in adult red cells to give human hemoglobin HbA in amounts equal to or greater than endogenous mouse hemoglobin. Expression of HbA in murine red cells is not accompanied by any increase in mean corpuscular volume (MCV) or mean corpuscular hemoglobin concentration (MCHC). However, these transgenic mice tend to have an increased number of reticulocytes in peripheral blood; consistent with some degree of hemolysis. Metabolic labeling experiments showed balanced mouse globin synthesis, but imbalanced human globin synthesis, with an alpha/beta biosynthetic ratio of approximately 0.6. Thus, these mice have mild anemia. These results are discussed with relation to the coordinate regulation of alpha- and beta-globin synthesis in erythroid tissues.

Cloning and expression of human salivary-gland kallikrein in Escherichia coli

CDNA clones for human kallikrein have been identified in a cDNA library constructed from mRNA of human salivary gland. The entire coding sequence for preprokallikrein and for the 5'- and 3'-untranslated regions were isolated by using a mixture of oligonucleotides corresponding to amino acids 51-56 of human urinary kallikrein and one oligonucleotide corresponding to amino acids 233-238 of human pancreatic kallikrein. The DNA sequence proved that, with the exception of two amino acid exchanges, kallikrein of the human salivary gland is identical with pancreatic kallikrein. Salivary gland and renal kallikrein was expressed in Escherichia coli from plasmid pKK223-3 under the control of the tac promoter. The protein was identified by Western-blot analysis and by demonstration of its specific proteolytic activity.

Alterations in the expression and gating of Drosophila sodium channels by mutations in the para gene

Mutations in the para gene specifically affect the expression of sodium currents in Drosophila. While 65% of wild-type embryonic neurons in culture express sodium currents, three distinct mutations in the para locus resulted in a decrease in the fraction of cells from which sodium currents could be recorded. This reduction was allele-dependent: macroscopic sodium currents were exhibited in 49% of the neurons in parats1 cultures, 35% in parats2, and only 2% in paraST76. Voltage-clamp experiments demonstrated that the parats2 mutation also affected the gating properties of sodium channels. These results provide convincing evidence that para, a gene recently shown to exhibit sequence similarity to vertebrate sodium channels alpha subunits, encodes functional sodium channels in Drosophila. The finding that one para allele (paraST76) can virtually eliminate the expression of sodium currents strongly argues that the para gene codes for the majority of sodium channels in cultured embryonic neurons.

Isolation and characterization of the human parathyroid hormone-like peptide gene

A parathyroid hormone-like peptide (PTH-LP) has recently been identified in human tumors associated with the syndrome of humoral hypercalcemia of malignancy. The peptide appears to be encoded by a single-copy gene that gives rise to multiple mRNAs that are heterogeneous at both their 5' and their 3' ends. Alternative RNA splicing is responsible for the 3' heterogeneity and results in mRNAs encoding three different peptides, each with a unique C terminus. We have isolated and characterized the human PTHLP gene. The gene is a complex transcriptional unit spanning more than 12 kilobases of DNA and containing six exons. Two 5' exons encode distinct 5' untranslated regions and are separated by a putative promoter element, indicating that the gene either has two promoter or is alternatively spliced from a single promoter upstream of the first exon. The middle portion of the PTHLP gene, comprising exons 2-4, has an organizational pattern of introns and exons identical to that of the parathyroid hormone gene, consistent with a common ancestral origin of these two genes. Exon 4 of the PTHLP gene encodes the region common to all three peptides and the C terminus of the shortest peptide, and exons 5 and 6 encode the unique C termini of the other two peptides. Northern analysis of mRNAs from four human tumors of different histological types reveals the preferential use of 3' splicing patterns by individual tumors.